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A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Sheffield NC, Song H, Cameron SL, Whiting MF - Mol. Biol. Evol. (2008)

Bottom Line: We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency.All six species of beetle have the same gene order as the ancestral insect.We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, USA. ncs@byu.net

ABSTRACT
Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

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Consensus secondary cloverleaf structure for the tRNA-Ser(AGN) gene for all 13 published coleopteran genomes. Capitalized bases are conserved in at least 12 of the 13 sequences; lowercase bases are majority rule. Base pairs may not necessarily match because bases are majority rule.
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fig6: Consensus secondary cloverleaf structure for the tRNA-Ser(AGN) gene for all 13 published coleopteran genomes. Capitalized bases are conserved in at least 12 of the 13 sequences; lowercase bases are majority rule. Base pairs may not necessarily match because bases are majority rule.

Mentions: In insect mtgenomes, there are typically 22 tRNAs, with tRNA-Ser and tRNA-Leu 8-fold redundant (two sets of 4-fold redundant tRNAs) (Boore 1999). The length of tRNAs ranged between 60 bp and 75 bp. When compared across all beetle species, including the previously published mtgenomes, we found that the tRNAs were highly conserved within Coleoptera and that all the anticodons were identical and completely conserved, with one exception: the tRNA-Ser(AGN). This particular tRNA was also the most difficult to locate and fold using conventional tRNA search methods such as tRNAscan-SE because it often does not fold into a normal cloverleaf structure due to the absence of stem pairings in the DHU arm (fig. 6). This missing D-stem has been reported in insects (Beard et al. 1993; Crozier RH and Crozier YC 1993; Shao and Barker 2003; Bae et al. 2004), mammals (Chimnaronk et al. 2005; Putz et al. 2007), as well as the rest of Metazoa (Steinberg and Cedergren 1994). Garey and Wolstenholme (1989) proposed that the missing D-stem in tRNA-Ser(AGN) evolved very early in the evolution of Metazoa. Despite lacking this stem, however, this tRNA is normally considered to be functional (Steinberg and Cedergren 1994; Stewart and Beckenbach 2003). In an in vitro study, Hanada et al. (2001) found that bovine tRNA-Ser(AGN) (which lacks the D-stem) is functional, although somewhat less effective than other cloverleaf-shaped tRNAs.


A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Sheffield NC, Song H, Cameron SL, Whiting MF - Mol. Biol. Evol. (2008)

Consensus secondary cloverleaf structure for the tRNA-Ser(AGN) gene for all 13 published coleopteran genomes. Capitalized bases are conserved in at least 12 of the 13 sequences; lowercase bases are majority rule. Base pairs may not necessarily match because bases are majority rule.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2568038&req=5

fig6: Consensus secondary cloverleaf structure for the tRNA-Ser(AGN) gene for all 13 published coleopteran genomes. Capitalized bases are conserved in at least 12 of the 13 sequences; lowercase bases are majority rule. Base pairs may not necessarily match because bases are majority rule.
Mentions: In insect mtgenomes, there are typically 22 tRNAs, with tRNA-Ser and tRNA-Leu 8-fold redundant (two sets of 4-fold redundant tRNAs) (Boore 1999). The length of tRNAs ranged between 60 bp and 75 bp. When compared across all beetle species, including the previously published mtgenomes, we found that the tRNAs were highly conserved within Coleoptera and that all the anticodons were identical and completely conserved, with one exception: the tRNA-Ser(AGN). This particular tRNA was also the most difficult to locate and fold using conventional tRNA search methods such as tRNAscan-SE because it often does not fold into a normal cloverleaf structure due to the absence of stem pairings in the DHU arm (fig. 6). This missing D-stem has been reported in insects (Beard et al. 1993; Crozier RH and Crozier YC 1993; Shao and Barker 2003; Bae et al. 2004), mammals (Chimnaronk et al. 2005; Putz et al. 2007), as well as the rest of Metazoa (Steinberg and Cedergren 1994). Garey and Wolstenholme (1989) proposed that the missing D-stem in tRNA-Ser(AGN) evolved very early in the evolution of Metazoa. Despite lacking this stem, however, this tRNA is normally considered to be functional (Steinberg and Cedergren 1994; Stewart and Beckenbach 2003). In an in vitro study, Hanada et al. (2001) found that bovine tRNA-Ser(AGN) (which lacks the D-stem) is functional, although somewhat less effective than other cloverleaf-shaped tRNAs.

Bottom Line: We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency.All six species of beetle have the same gene order as the ancestral insect.We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, USA. ncs@byu.net

ABSTRACT
Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

Show MeSH